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Improving interoperability between microbial information and sequence databases

Paolo Romano, Peter Dawyndt, Francesca Piersigilli, Jean Swings
2005 BMC Bioinformatics  
Identification of links to sequence databases can be useful, but annotation and indexing problems, together with compilation errors, immediately arise.  ...  Conclusion: Links between EMBL and CABRI catalogues constitute an improved access to microorganisms of certified quality and can produce positive effects on biomedical research.  ...  Acknowledgements This work was partially supported by the "European Biological Resource Centres Network" project, funded by the European Union in the frame of the "Quality of life and management of living  ... 
doi:10.1186/1471-2105-6-s4-s23 pmid:16351750 pmcid:PMC1866384 fatcat:dovfpewrqfhv3nhbkbtlntg6va

An Information System for European culture collections: the way forward

Serge Casaregola, Alexander Vasilenko, Paolo Romano, Vincent Robert, Svetlana Ozerskaya, Anna Kopf, Frank O. Glöckner, David Smith
2016 SpringerPlus  
Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible.  ...  Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently.  ...  Analysis of the data provision requests from users can be separated into two main categories: (1) availability of improved and reliable metadata, and (2) improved interoperability between databases.  ... 
doi:10.1186/s40064-016-2450-8 pmid:27386258 pmcid:PMC4912550 fatcat:sckraiy3wzh6jfsb4u5jpcyj6q

Report On Workshop And Surveys On Current Collection Status Of Data Management Systems, Metadata Sources, Semantic Systems, And Molecular, Taxonomy, Nomenclature, Bibliography And Environmental Databases To Be Considere D By The Platform

Paolo Romano, Daniele Pierpaolo Colobraro
2014 Zenodo  
management of and an advanced access to culture collection data, - the information systems that relate to the microbiological domain and should interoperate with the MIRRI-IS.  ...  In the first report, deliverable D8.1, the MIRRI Information System (MIRRI-IS) vision and strategy was introduced.  ...  Public databases and information systems related to microbial resources Many public information systems and databases exist that may support, in tight connection with mBRC databases, the proposed downstream  ... 
doi:10.5281/zenodo.154637 fatcat:cx3kouposzcirll2w5ukhfxn4e

Micado—a network-oriented database for microbial genomes

Véronique Biaudet, Franck Samson, Philippe Bessières
1997 Bioinformatics  
It links eubacterial and archaeal sequences, genetic maps for Bacillus subtilis and Escherichia coli, and information on mutants.  ...  We have automated imports of microbial sequences, and E.coli genetic map, by programming parsers of flat file distributions.  ...  Acknowledgements We thank Dusko Ehrlich for his active support and contribution to the project, Shahinaz Gas and Jakub Zimmermann, students involved in the development of the database, the B.subtilis community  ... 
doi:10.1093/bioinformatics/13.4.431 fatcat:rmmqim4m65a7dinbo4wpkeebdy

The MAR databases: development and implementation of databases specific for marine metagenomics

Terje Klemetsen, Inge A Raknes, Juan Fu, Alexander Agafonov, Sudhagar V Balasundaram, Giacomo Tartari, Espen Robertsen, Nils P Willassen
2017 Nucleic Acids Research  
Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information.  ...  All contextual and sequence databases are freely accessible and downloadable from  ...  ACKNOWLEDGEMENTS We thank all the experts who contributed to the MMP database annotations from their field of expertise, especially ELIXIR EXCELERATE WP6 partners.  ... 
doi:10.1093/nar/gkx1036 pmid:29106641 pmcid:PMC5753341 fatcat:wgg4tz754zcebam7dvtoddoawm

Bioinformatics activities at the University Hospital San Martino IST in Genoa

Paolo DM Romano
2017 EMBnet journal  
When the EMBL Nucleotide Sequence Data Library was first established, in 1980, the challenges mainly related to establishing the first databases and developing sequence comparison algorithms.  ...  With SRS, data must reside locally and be stored in 'flat files' (text-only files) with pre-defined, shared syntaxes. Both explicit and implicit links between databases can be defined.  ... 
doi:10.14806/ej.23.0.884 fatcat:x534vlgbezcd5mainfea57cylu

Skerman and beyond: 2019 status of the Global Catalogue of Microorganisms

Juncai Ma, Linhuan Wu, İpek Kurtböke
2019 Microbiology Australia  
As a result, the WDCM is now facilitating the application of cutting-edge information technology to improve the interoperability of microbial data, promote the access to and use of data and information  ...  In the advance stage of the GCM 2 development the following points are targeted: (1) From strain data to 'omics' data and to improved database platform, (2) from database to knowledge base and to improved  ... 
doi:10.1071/ma19033 fatcat:oql27avhy5dsvct6ulabm2orhi

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu
2016 Database: The Journal of Biological Databases and Curation  
of mining information from millions of full-text articles, (ii) the 'interoperability' issue of integrating various text-mining systems into existing curation workflows and (iii) the 'reusability' issue  ...  Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.  ...  Figure 1 . 1 Interconnection between literature services and biological databases.  ... 
doi:10.1093/database/baw161 pmid:28025348 pmcid:PMC5199160 fatcat:q22gw7owfjejznsrom3c4xnlem

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform

Adrian Egli, Dominique S. Blanc, Gilbert Greub, Peter M. Keller, Vladimir Lazarevic, Aitana Lebrand, Stephen Leib, Richard A. Neher, Vincent Perreten, Alban Ramette, Jacques Schrenzel, Roger Stephan (+3 others)
2018 Swiss Medical Weekly  
In addition, high quality sequence data are a key element between centres using WGS data for diagnostic and epidemiological applications.  ...  However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and curated metadata are a key requirement for fully understanding this complexity.  ...  , initiatives, and analytical tools using whole genome sequence information from pathogens Weblink Database Global microbial identifier Compare  ... 
doi:10.4414/smw.2018.14693 fatcat:fb2rjqb7jncvpnx4p4tve7hmsq

The next meta-challenge for Bioinformatics

Willy Valdivia-Granda
2008 Bioinformation  
The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes.  ...  metagenomic information into biomedical, agricultural, environmental, and industrial applications.  ...  Mya Breitbart and Francis Larson for the insightful comments and suggestions. The genomic barcoding technology is partially supported by the Defense Threat Reduction Agency.  ... 
doi:10.6026/97320630002358 pmid:18685725 pmcid:PMC2478737 fatcat:vcivjjwhcjf3leqgy4sw4qov7m

Bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform

Jonas Marschall
2019 Swiss Medical Weekly  
Interoperable and curated metadata area key requirement for fully understanding this complexity.In addition, high quality sequence data are a key elementbetween centres using WGS data for diagnostic and  ...  Thespread of highly virulent and resistant pathogens can bedescribed using molecular typing technologies; in particu-lar, whole genome sequencing (WGS) data can be usedfor molecular typing purposes with  ...  , initiatives, and analytical tools using whole genome sequence information from pathogens Weblink Database Global microbial identifier Compare  ... 
doi:10.4414/smw.2019.14707 fatcat:ujwfozpemvctzellzzwfit5cpi

BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis

Lorenz Christian Reimer, Anna Vetcininova, Joaquim Sardà Carbasse, Carola Söhngen, Dorothea Gleim, Christian Ebeling, Jörg Overmann
2018 Nucleic Acids Research  
With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains.  ...  A revised graphical user interface and new search tools such as the API® test finder, the TAXplorer, or the Microbial Isolation Source Search significantly improve the user experience.  ...  On the data level, interoperability is attained by applying standards and stable identifiers like INSDC sequence accession numbers (10) for sequence data, culture collection numbers for microbial strains  ... 
doi:10.1093/nar/gky879 pmid:30256983 pmcid:PMC6323973 fatcat:eq6b3t4o7nennldlg5n6db4imy

D8.4_Mirri_Report On Comparison Of Various Integration Software Operating In Life Sciences

B. Bunk, DP Colobraro, P. Dawyndt, P. De Vos, F.O. Glöckner, A. Kopf, V. Robert, P. Romano, D. Smith, C. Söhngen, F. Van Hauwenhuyse, A. Vasilenko
2015 Zenodo  
The objective of this deliverable is the analysis of some data integration architectures and tools in Life Sciences to determine their respective advantages and disadvantages in meeting the objectives  ...  two sections: 'Get microbial data' and 'Retrieve external information'.  ...  Thanks to the inclusion of nucleotide and protein sequences in GCM, sequence alignments between various strains, generally at species level, are possible.  ... 
doi:10.5281/zenodo.49968 fatcat:72fy55qtjfgbrecrkslp25s5he

Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens

Ruth E. Timme, William J. Wolfgang, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, Marc Allard, Errol Strain
2020 One Health Outlook  
Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow.  ...  And finally, we provide curation guidance and an SOP for keeping your public data current within the database.  ...  We also thank our Genometrakr collaborators (including CDC, FSIS, NCBI, and David Lipman) for reviewing the manuscript and providing feedback prior to publication.  ... 
doi:10.1186/s42522-020-00026-3 pmid:33103064 pmcid:PMC7568946 fatcat:yfexo6xtobcm3ffw3gexlxlg2u

ELIXIR-EXCELERATE D6.5: Improvement and Application of Eukaryotic Gene catalogue

Eric Pelletier, Erwan Corre, Guita Niang, Arnaud Meng, Mark Hoebeke, Robert Finn
2019 Zenodo  
Thereapplicationhighlightsthere-useofCWLtooldescriptions and the outputs of the Compute (WP4) and Interoperability platforms (WP5), and demonstrates how workflows can be used to make new data resources  ...  This new resource dramatically increases the representation of micro-eukaryotic organisms, both in this new database, as well as being propagated to core data resources such as ENA and UniProtKB.  ...  Task 6.2 will be achieved by establishing marine microbial databases including reference genomes, nucleotide and protein databases.  ... 
doi:10.5281/zenodo.3234521 fatcat:hd3lxdjedjbldothtk5mz26wue
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